@inproceedings{fedba43745fa439c9926735ce0137a44,
title = "Identifying Structural Changes in Correlation Networks Models of Cancer Gene Expression by Stage",
abstract = "Gene expression analysis using correlation network modeling can help to identify systems-level cellular changes and cooperation among genes. Network modeling is a relatively novel method for comparing changes across stages of cancer, or between primary tumor tissue and the metastatic tissue. In this study, we develop a pipeline to identify the dynamic changes of cancer in gene expression level through time-dependent network analysis of cancer data from The Cancer Genome Atlas (TCGA). A total of 16 correlation networks were built from four (4) stages in four (4) different types of cancers: Thyroid Carcinoma, Colon Adenocarcinoma and Rectum Adenocarcinoma, Stomach Adenocarcinoma, and Kidney Renal Clear Cell Carcinoma. To identify the basic changes in network structure, we performed Jaccard similarity comparison of structurally relevant nodes. We employed mutation analysis to measure and present the time-based changes in mutation rate of genes that are specific to each cancer type. Finally, we present a case study to identify the gene expression changes among primary tumor tissue and metastatic tissue in skin cutaneous melanoma (SKCM).",
keywords = "Correlation networks, Gene expression, Jaccard Similarity, The Cancer Genome Atlas, mutation rates",
author = "Qianran Li and Dario Ghersi and Ishwor Thapa and Ling Zhang and Hesham Ali and Kate Cooper",
note = "Publisher Copyright: {\textcopyright} 2019 IEEE.; 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019 ; Conference date: 18-11-2019 Through 21-11-2019",
year = "2019",
month = nov,
doi = "10.1109/BIBM47256.2019.8983069",
language = "English (US)",
series = "Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "2075--2082",
editor = "Illhoi Yoo and Jinbo Bi and Hu, {Xiaohua Tony}",
booktitle = "Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019",
}